Thomas R. Stanley

SMALL‐MAMMAL DENSITY ESTIMATION: A FIELD COMPARISON OF GRID‐BASED VS. WEB‐BASED DENSITY ESTIMATORS

Statistical models for estimating absolute densities of field populations of animals have been widely used over the last century in both scientific studies and wildlife management programs. To date, two general classes of density estimation models have been developed: models that use data sets from capture–recapture or removal sampling techniques (often derived from trapping grids) from which separate estimates of population size (N) and effective sampling area (Â) are used to calculate density (D = N/Â); and models applicable to sampling regimes using distance-sampling theory (typically transect lines or trapping webs) to estimate detection functions and densities directly from the distance data. However, few studies have evaluated these respective models for accuracy, precision, and bias on known field populations, and no studies have been conducted that compare the two approaches under controlled field conditions. In this study, we evaluated both classes of density estimators on known densities of e...

A closure test for time-specific capture-recapture data

The assumption of demographic closure in the analysis of capture-recapture data under closed-population models is of fundamental importance. Yet, little progress has been made in the development of omnibus tests of the closure assumption. We present a closure test for time-specific data that, in principle, tests the null hypothesis of closed-population model Mt against the open-population Jolly-Seber model as a specific alternative. This test is chi-square, and can be decomposed into informative components that can be interpreted to determine the nature of closure violations. The test is most sensitive to permanent emigration and least sensitive to temporary emigration, and is of intermediate sensitivity to permanent or temporary immigration. This test is a versatile tool for testing the assumption of demographic closure in the analysis of capture-recapture data.

Host and viral ecology determine bat rabies seasonality and maintenance

Rabies is an acute viral infection that is typically fatal. Most rabies modeling has focused on disease dynamics and control within terrestrial mammals (e.g., raccoons and foxes). As such, rabies in bats has been largely neglected until recently. Because bats have been implicated as natural reservoirs for several emerging zoonotic viruses, including SARS-like corona viruses, henipaviruses, and lyssaviruses, understanding how pathogens are maintained within a population becomes vital. Unfortunately, little is known about maintenance mechanisms for any pathogen in bat populations. We present a mathematical model parameterized with unique data from an extensive study of rabies in a Colorado population of big brown bats (Eptesicus fuscus) to elucidate general maintenance mechanisms. We propose that life history patterns of many species of temperate-zone bats, coupled with sufficiently long incubation periods, allows for rabies virus maintenance. Seasonal variability in bat mortality rates, specifically low mortality during hibernation, allows long-term bat population viability. Within viable bat populations, sufficiently long incubation periods allow enough infected individuals to enter hibernation and survive until the following year, and hence avoid an epizootic fadeout of rabies virus. We hypothesize that the slowing effects of hibernation on metabolic and viral activity maintains infected individuals and their pathogens until susceptibles from the annual birth pulse become infected and continue the cycle. This research provides a context to explore similar host ecology and viral dynamics that may explain seasonal patterns and maintenance of other bat-borne diseases.

INTERACTION OF BEAVER AND ELK HERBIVORY REDUCES STANDING CROP OF WILLOW

Populations of beaver and willow have not thrived in riparian environments that are heavily browsed by livestock or ungulates, such as elk. The interaction of beaver and elk herbivory may be an important mechanism underlying beaver and willow declines in this competitive environment. We conducted a field experiment that compared the standing crop of willow three years after simulated beaver cutting on paired plants with and without intense elk browsing (∼85% utilization rate). Simulated beaver cutting with intense elk browsing produced willow that was small (biomass and diameter) and short, with far fewer, but longer, shoots and a higher percentage of dead biomass. In contrast, simulated beaver cutting without elk browsing produced willow that was large, tall, and leafy, with many more, but shorter, shoots (highly branched) and a lower percentage of dead biomass. Total stem biomass after three years was 10 times greater on unbrowsed plants than on browsed plants. Unbrowsed plants recovered 84% of their pr...

MODELING AND ESTIMATION OF STAGE-SPECIFIC DAILY SURVIVAL PROBABILITIES OF NESTS

In studies of avian nesting success, it is often of interest to estimate stage-specific daily survival probabilities of nests. When data can be partitioned by nesting stage (e.g., incubation stage, nestling stage), piecewise application of the Mayfield method or Johnsons method is appropriate. However, when the data contain nests where the transition from one stage to the next occurred during the interval between visits, piecewise approaches are inappropriate. In this paper, I present a model that allows joint estimation of stage-specific daily survival probabilities even when the time of transition between stages is unknown. The model allows interval lengths between visits to nests to vary, and the exact time of failure of nests does not need to be known. The performance of the model at various sample sizes and interval lengths between visits was investigated using Monte Carlo simulations, and it was found that the model performed quite well: bias was small and confidence-interval coverage was at the nominal 95% rate. A SAS program for obtaining maximum likelihood estimates of parameters, and their standard errors, is provided in the Appendix.

Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot

Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds.

Estimator Selection for Closed-Population Capture: Recapture

For valid statistical inference, it is important to select an appropriate statistical model. In the analysis of capture-recapture data under the closed-population models of Otis et al. (1978), information theoretic and hypothesis testing approaches to model selection are not practical, because some of the models have likelihoods with nonidentifiable parameters. A further problem is that, for some of the Otis et al. models, multiple estimators exist but there is no objective basis for deciding which estimator to use for a particular dataset. In CAPTURE, a computer program for estimating parameters under the closed models of Otis et al., a linear discriminant classifier is used to select an appropriate model. This classifier frequently selects the incorrect generating model in simulation studies, and it provides no guidance on which estimator to use once a model has been selected. In this study, we develop new classifiers for selecting the best estimator (as opposed to the generating model) and evaluate their performance. In addition, we investigate an estimator averaging approach to estimation that is a modification of the model averaging approach described by Buckland et al. (1997). We found that, in general, the overall performance of the new classifiers was unimpressive. In contrast, the estimator averaging approach we investigated performed well.

Adult survival and population growth rate in Colorado big brown bats (Eptesicus fuscus)

Abstract We studied adult survival and population growth at multiple maternity colonies of big brown bats (Eptesicus fuscus) in Fort Collins, Colorado. We investigated hypotheses about survival using information-theoretic methods and mark–recapture analyses based on passive detection of adult females tagged with passive integrated transponders. We constructed a 3-stage life-history matrix model to estimate population growth rate (λ) and assessed the relative importance of adult survival and other life-history parameters to population growth through elasticity and sensitivity analysis. Annual adult survival at 5 maternity colonies monitored from 2001 to 2005 was estimated at 0.79 (95% confidence interval [95% CI] = 0.77–0.82). Adult survival varied by year and roost, with low survival during an extreme drought year, a finding with negative implications for bat populations because of the likelihood of increasing drought in western North America due to global climate change. Adult survival during winter was higher than in summer, and mean life expectancies calculated from survival estimates were lower than maximum longevity records. We modeled adult survival with recruitment parameter estimates from the same population. The study population was growing (λ = 1.096; 95% CI = 1.057–1.135). Adult survival was the most important demographic parameter for population growth. Growth clearly had the highest elasticity to adult survival, followed by juvenile survival and adult fecundity (approximately equivalent in rank). Elasticity was lowest for fecundity of yearlings. The relative importances of the various life-history parameters for population growth rate are similar to those of large mammals.

Bat ecology and public health surveillance for rabies in an urbanizing region of Colorado

We describe use of Fort Collins, Colorado, and nearby areas by bats in 2001–2005, and link patterns in bat ecology with concurrent public health surveillance for rabies. Our analyses are based on evaluation of summary statistics, and information-theoretic support for results of simple logistic regression. Based on captures in mist nets, the city bat fauna differed from that of the adjacent mountains, and was dominated by big brown bats (Eptesicus fuscus). Species, age, and sex composition of bats submitted for rabies testing locally and along the urbanizing Front Range Corridor were similar to those of the mist-net captures and reflected the annual cycle of reproduction and activity of big brown bats. Few submissions occurred November- March, when these bats hibernated elsewhere. In summer females roosted in buildings in colonies and dominated health samples; fledging of young corresponded to a summer peak in health submissions with no increase in rabies prevalence. Roosting ecology of big brown bats in buildings was similar to that reported for natural sites, including colony size, roost-switching behavior, fidelity to roosts in a small area, and attributes important for roost selection. Attrition in roosts occurred from structural modifications of buildings to exclude colonies by citizens, but without major effects on long-term bat reproduction or survival. Bats foraged in areas set aside for nature conservation. A pattern of lower diversity in urban bat communities with dominance by big brown bats may occur widely in the USA, and is consistent with national public health records for rabies surveillance.

Software Review: A program for testing capture-recapture data for closure

Abstract Capture–recapture methods are widely used to estimate population parameters of free-ranging animals. Closed-population capture-recapture models, which assume there are no additions to or losses from the population over the period of study (i.e., the closure assumption), are preferred for population estimation over the open-population models, which do not assume closure, because heterogeneity in detection probabilities can be accounted for and this improves estimates. In this paper we introduce CloseTest, a new Microsoft® Windows-based program that computes the Otis et al. (1978) and Stanley and Burnham (1999) closure tests for capture–recapture data sets. Information on CloseTest features and where to obtain the program are provided.